GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Bacteroides thetaiotaomicron VPI-5482

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 351606 BT2078 dihydroxy-acid dehydratase (NCBI ptt file)

Query= reanno::pseudo5_N2C3_1:AO356_24585
         (578 letters)



>FitnessBrowser__Btheta:351606
          Length = 600

 Score =  216 bits (549), Expect = 3e-60
 Identities = 171/578 (29%), Positives = 275/578 (47%), Gaps = 65/578 (11%)

Query: 5   KPSLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIA 64
           K  LRS+  F T  +     R+     G+  +Q  GKPII I N++++  P + H  +I 
Sbjct: 2   KKQLRSS--FSTQGRRMAGARALWAANGMKKNQM-GKPIIAIVNSFTQFVPGHVHLHEIG 58

Query: 65  EHVKRGVIEAGGFPVEFPVFSNGES-NLRPTAML----TRNLASMDVEEAIRGNPIDGVV 119
           + VK  + + G F  EF   +  +   +    ML    +R++ +  VE  +  +  D +V
Sbjct: 59  QLVKAEIEKLGCFAAEFNTIAIDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHKADAMV 118

Query: 120 LLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTIT 179
            ++ CDK TP +LM A   ++P + V+GGPM  G+  GQ +        +   +K+   +
Sbjct: 119 CISNCDKITPGMLMAAMRLNIPTVFVSGGPMEAGEWNGQHLDL------IDAMIKSADDS 172

Query: 180 IDDFLAA--EGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAH-- 235
           + D   A  E     + G C+ M TA++M C+ EA+G +LP N  I A    R  L    
Sbjct: 173 VSDQEVANIEQNACPTCGCCSGMFTANSMNCLNEAIGLALPGNGTIVATHENRTKLFEDA 232

Query: 236 -----MSGMRAVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVQ 290
                 + M+  E   E +    I T++AF NA+ ++ A+GGSTN V+HL A+A   GV 
Sbjct: 233 AKLIVENAMKYYEEGDESVLPRSIATRQAFLNAMTLDIAMGGSTNTVLHLLAVAHEAGVD 292

Query: 291 LDLDDWTRIGRGMPTIVDLQP-SGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNG 349
             +DD   + R  P +  + P + ++ +++   AGG+ A+L  L +  LI + + L V+G
Sbjct: 293 FKMDDIDMLSRKTPCLCKVAPNTQKYHIQDVNRAGGIIAILAELAKGGLI-DTSVLRVDG 351

Query: 350 KSLGENTKDAPI------------------------------YGQD-------EVIRTLD 372
            SL E      I                              Y Q+         IR L+
Sbjct: 352 MSLAEAIDQYSITSPNVTEKAMSKYSSAAGNRFNLVLGSQGAYYQELDKDRANGCIRDLE 411

Query: 373 NPIRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPELDVD 432
           +    DGG+ VL+GN+A  G V+K +     + +  G A VF++ +     I      V 
Sbjct: 412 HAYSKDGGLAVLKGNIAQDGCVVKTAGVDESIWKFTGPAKVFDSQEAACEGILGGR--VV 469

Query: 433 ANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVVLHVAP 492
           +  ++V+ + GPKG PGM E+       K    G  +   I+D R SG   G  + HV+P
Sbjct: 470 SGDVVVITHEGPKGGPGMQEMLYPTSYIKSRHLG-KECALITDGRFSGGTSGLSIGHVSP 528

Query: 493 EAAAGGPLAAVKEGDWIELDCASGRLHLDIPDAELAAR 530
           EAAAGG +  + +GD IE+D  +  +++ + D ELAAR
Sbjct: 529 EAAAGGNIGKIVDGDIIEIDIPARTINVRLTDEELAAR 566


Lambda     K      H
   0.319    0.136    0.409 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 779
Number of extensions: 35
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 578
Length of database: 600
Length adjustment: 37
Effective length of query: 541
Effective length of database: 563
Effective search space:   304583
Effective search space used:   304583
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory